Thursday, February 19, 2015

Well, got an email invite to one of these Oxford Global Meetings. Sadly the gender ratio of listed speakers is awful. I highlighted the list below (men in yellow, women in green). Ratio of 17:3. (See below). No thanks Oxford Global.

Thanks PeerJ and all the co-authors for their great work. I love open science and I particularly think we need continuing experiments on the best ways to do open science. Thus I like the experiment that is PeerJ in regard to how to publish and how to pay for open access fees.

I plugged in my headphones (was not sure if my kids should hear it) and listened away. And what I heard was excrutiatingly painful. The CBC Fresh Air reporter was discussing kissing and the microbiome with JA Tetro. And Tetro made some of the most misleading, ridiculous overstatements about the microbiome I have heard in many years:

He basically implied or specifically said that, in humans, attraction to partners and relationship success was determined by finding a partner with similar microbiomes to oneself.

Furthermore he discussed how maintaining similar microbiomes (e.g., via consuming the same probiotics or fermented foods) would help maintain attraction and how things like travel away from a partner might lead to repulsion.

He said things like tha our immune systems determine if a partner is right for you from kiss-based comparison of a partner's microbiome to one's own.

And that if the microbiome in a kissing partner is a match this leads to bliss and addiction and that salive is the first line of defense when it comes to relationships.

He even went so far as to say that this is all about "trying to find your mother because our microbiomes come from our mother."

I could do on and on. It was the worst, most misleading, innacurate material I have probably ever heard about microbiomes. Tetro and CBC Fresh Air should be ashamed.

Tetro says that when you kiss your date, his or her germs make their way into your mouth’s ecosystem. And if it’s a match, you’ll want to keep smooching.

“This study does one amazing thing, it shows you that kissing is the best way to find a mate for the long term. It might sound really gross but if the bacteria from the other person harmonizes with your bacteria, your immune system is all good. You feel a sense of calm and happiness, maybe even addiction,” he explained.

“But if the bacteria don’t align with your microbes, you actually feel disgust and revolt. Your immune system is rejecting that person as a possible mate.”

and

“This study proves that when it comes to finding the right mate, the old game of spin the bottle actually has a base in science,” he said.

More completely inaccurate, made up material with no basis in science. As far as I can tell, this is basically made up. Sure there may be a theory behind this. But to present it as established facts about the microbiome is ridiculous.

This is all a shame really since the paper which the CBC Fresh Air story is referring to is actually a perfectly fine paper and the authors of the paper do not seem to be pushing these over the top ridiculous ideas. And for this terrible story I am giving CBC Fresh Air and JA Tetro an "Overselling the microbiome award".

Thursday, February 12, 2015

It has one of the worst microbe-evolution sections of text I have seen in a long long time:

Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly.

But the relationship of antibiotics to mitochondria may go back a long way. In evolution, mitochondria descended from bacteria, which were some of the earliest life forms, and different bacteria competed with each other for survival. That an antibiotic would still selectively attack the portion of a cell that most closely resembles bacteria may be a throwback to that ingrained sense of competition and the very evolution of life.

Yup. That antibiotics that target bacteria also affect mitochondria is a throwback to that ingrained sense of competition and the very evolution of life.

I guess I had hoped that perhaps they would try to change their practices after I and other people criticized them for their past record. So - I went to the web site for the ICG10 meeting advertised in the Tweet. Oh well, silly me for hoping.

On the front page they have 14 speakers they are promoting - all of them male.

Screen shot from ICG10 web site

On the announcement page they have a slightly different list where the ratio is 14:1

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”

And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today: Don’t ignore the science Davis Enterprise. I quote from it below:

The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.”

Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?

He completely nailed it here. I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.
-----------------------------------

In August 2014, the American Academy of Pediatrics released a scientific sleep study report that recommended an 8:30 am start time for schools, which would allow secondary students more time to sleep. The report generated community discussions and concerns since Davis secondary schools start before 8:30 am.
In response, the superintendent initiated the formation of a Sleep Study Committee (made up of students, teachers, counselors, parent/community members and administrators) to examine the benefits and logistical challenges of an earlier school start.

This update is a report of the formation of the Sleep Study Committee and their charge. For reiteration, at this time, staff is not offering recommendations about a modified start time. Staff will wait to review the work of the Sleep Study Committee before offering formal recommendations to the Board.

So I started digging around for more on the topic and found some things worth reading But the most interesting thing I found was that there has been a discussion about this exact issue in the county where I grew up: Montgomery County Maryland. Some of the articles about this area listed below:

It seems to me that Davis, CA really needs to consider this as a possibility. It could help students in many ways and seems to be a relatively easy (though not free of course) way to improve the lives and learning of students in our town. I am thrilled that the Board is bringing the topic up again. Any examples out there of places that have shifted start times based on the AAP recommendation would be great (and what happened ...).

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills. The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems. Experience in the analysis of environmental sequence data is highly desirable, but not required.

The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references
Submit materials to ie2jobs@uoregon.edu. Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.